R Notebook

List of all input files

/home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/JW_BC1/all_NNNATTAGC_L5Ab_BC1_rnc-HTF_1.unique.hyb.p_values.tab /home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/JW_BC1/all_NNNCACTAGC_L5Bc_BC1_rnc-HTF_3.unique.hyb.p_values.tab /home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/JW_BC1/all_NNNGCGCAGC_L5Ac_BC1_rnc-HTF-2.unique.hyb.p_values.tab

list_of_files

$DM_MiSeq_Bc
[1] "/home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/DM_MiSeq/all_NNNCACTAGC_L5Bc_rnc-HTF_1.unique.hyb.p_values.tab"

$DM_MiSeq_Bd
[1] "/home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/DM_MiSeq/all_NNNTCTCTAGC_L5Bd_rnc-HTF_2.unique.hyb.p_values.tab"

$DM_NextSeq_Bc
[1] "/home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/DM_NextSeq/all_NNNCACTAGC_L5Bc_rnc-HTF_1.unique.hyb.p_values.tab"

$DM_NextSeq_Bd
[1] "/home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/DM_NextSeq/all_NNNTCTCTAGC_L5Bd_rnc-HTF_2.unique.hyb.p_values.tab"

$JW_BC1_Ab
[1] "/home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/JW_BC1/all_NNNATTAGC_L5Ab_BC1_rnc-HTF_1.unique.hyb.p_values.tab"

$JW_BC1_Bc
[1] "/home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/JW_BC1/all_NNNCACTAGC_L5Bc_BC1_rnc-HTF_3.unique.hyb.p_values.tab"

$JW_BC1_Ac
[1] "/home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/JW_BC1/all_NNNGCGCAGC_L5Ac_BC1_rnc-HTF-2.unique.hyb.p_values.tab"

$JW_BC4_Bc
[1] "/home/ignatius/PostDoc/2020/StaphCLASH2020/Results/Hybrids_P_Values/JW_BC4/all_NNNCACTAGC_L5Bc_BC4_rnc-HTF_4.unique.hyb.p_values.tab"

list_of_tables <- purrr::map( list_of_files, vroom::vroom )

Rows: 21
Columns: 37
Delimiter: "\t"
chr [16]: left_hyb_id, left_rna_class, left_chromo, left_name, left_strand, right_hyb_id, right_rna_class, right_chromo, right_name, right_strand, left_transcript_start, l...
dbl [21]: g_x, left_hyb_count, left_genomic_start, left_genomic_stop, g_y, right_hyb_count, right_genomic_start, right_genomic_stop, smaller_max_depth, larger_max_depth, p...

Use `spec()` to retrieve the guessed column specification
Pass a specification to the `col_types` argument to quiet this message
Rows: 34
Columns: 37
Delimiter: "\t"
chr [16]: left_hyb_id, left_rna_class, left_chromo, left_name, left_strand, right_hyb_id, right_rna_class, right_chromo, right_name, right_strand, left_transcript_start, l...
dbl [21]: g_x, left_hyb_count, left_genomic_start, left_genomic_stop, g_y, right_hyb_count, right_genomic_start, right_genomic_stop, smaller_max_depth, larger_max_depth, p...

Use `spec()` to retrieve the guessed column specification
Pass a specification to the `col_types` argument to quiet this message
Rows: 26
Columns: 37
Delimiter: "\t"
chr [16]: left_hyb_id, left_rna_class, left_chromo, left_name, left_strand, right_hyb_id, right_rna_class, right_chromo, right_name, right_strand, left_transcript_start, l...
dbl [21]: g_x, left_hyb_count, left_genomic_start, left_genomic_stop, g_y, right_hyb_count, right_genomic_start, right_genomic_stop, smaller_max_depth, larger_max_depth, p...

Use `spec()` to retrieve the guessed column specification
Pass a specification to the `col_types` argument to quiet this message
Rows: 36
Columns: 37
Delimiter: "\t"
chr [16]: left_hyb_id, left_rna_class, left_chromo, left_name, left_strand, right_hyb_id, right_rna_class, right_chromo, right_name, right_strand, left_transcript_start, l...
dbl [21]: g_x, left_hyb_count, left_genomic_start, left_genomic_stop, g_y, right_hyb_count, right_genomic_start, right_genomic_stop, smaller_max_depth, larger_max_depth, p...

Use `spec()` to retrieve the guessed column specification
Pass a specification to the `col_types` argument to quiet this message
Rows: 653
Columns: 37
Delimiter: "\t"
chr [16]: left_hyb_id, left_rna_class, left_chromo, left_name, left_strand, right_hyb_id, right_rna_class, right_chromo, right_name, right_strand, left_transcript_start, l...
dbl [21]: g_x, left_hyb_count, left_genomic_start, left_genomic_stop, g_y, right_hyb_count, right_genomic_start, right_genomic_stop, smaller_max_depth, larger_max_depth, p...

Use `spec()` to retrieve the guessed column specification
Pass a specification to the `col_types` argument to quiet this message
Rows: 202
Columns: 37
Delimiter: "\t"
chr [16]: left_hyb_id, left_rna_class, left_chromo, left_name, left_strand, right_hyb_id, right_rna_class, right_chromo, right_name, right_strand, left_transcript_start, l...
dbl [21]: g_x, left_hyb_count, left_genomic_start, left_genomic_stop, g_y, right_hyb_count, right_genomic_start, right_genomic_stop, smaller_max_depth, larger_max_depth, p...

Use `spec()` to retrieve the guessed column specification
Pass a specification to the `col_types` argument to quiet this message
Rows: 420
Columns: 37
Delimiter: "\t"
chr [16]: left_hyb_id, left_rna_class, left_chromo, left_name, left_strand, right_hyb_id, right_rna_class, right_chromo, right_name, right_strand, left_transcript_start, l...
dbl [21]: g_x, left_hyb_count, left_genomic_start, left_genomic_stop, g_y, right_hyb_count, right_genomic_start, right_genomic_stop, smaller_max_depth, larger_max_depth, p...

Use `spec()` to retrieve the guessed column specification
Pass a specification to the `col_types` argument to quiet this message
Rows: 80
Columns: 37
Delimiter: "\t"
chr [16]: left_hyb_id, left_rna_class, left_chromo, left_name, left_strand, right_hyb_id, right_rna_class, right_chromo, right_name, right_strand, left_transcript_start, l...
dbl [21]: g_x, left_hyb_count, left_genomic_start, left_genomic_stop, g_y, right_hyb_count, right_genomic_start, right_genomic_stop, smaller_max_depth, larger_max_depth, p...

Use `spec()` to retrieve the guessed column specification
Pass a specification to the `col_types` argument to quiet this message

Remove tRNA, rRNA

List of all hybrids

Full join on itself

Overlap same orientation

Given Table of hybrids X and Table of hybrids Y, We join the table with the following rules: * left-hand-side of hybrid in Table X matches with left-hand-side of hybrid in Table Y, and * right-hand-side of hybrid in Table X matches with right-hand-side of hybrid in Table Y